6SIV: HPV16 E6 oncoprotein

Structure of HPV16 E6 oncoprotein in complex with mutant IRF3 LxxLL motif. Determined by X-ray diffraction at 1.75 Å resolution. Released 21 Aug 2019.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Escherichia coli (strain K12), Homo sapiens, Human papillomavirus type 16
Chains: 2
Atoms: 4,614
Mol. weight: 61.2 kDa
Ligands: ZN
Released: 21 Aug 2019

Explore 6SIV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SIV contains 39 α-helices and 36 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 27 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	8-11	4	1
α-helix	18-32	15
β-strand	36-39	4	1
α-helix	44-53	10
β-strand	60-64	5	1
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	2
α-helix	78-79	2
β-strand	80	1	3
α-helix	84-87	4
β-strand	90	1	4
α-helix	92-97	6
β-strand	99-100	2	3
β-strand	103-104	2	3
β-strand	107-112	6	1
β-strand	115-119	5	5
β-strand	129	1	6
α-helix	130-132	3
α-helix	133-141	9
β-strand	146-148	3	5
α-helix	155-164	10
β-strand	168-173	6	7
β-strand	176-183	8	7
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	5
α-helix	230-232	3
α-helix	233-238	6
β-strand	243-246	4	5
α-helix	247-249	3
β-strand	250	1	6
β-strand	251	1	8
β-strand	254	1	8
α-helix	255-256	2
α-helix	258	1
β-strand	259-260	2	9
β-strand	261-267	7	1
β-strand	268	1	2
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	1
β-strand	305	1	4
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	9
α-helix	331-332	2
α-helix	337-352	16
α-helix	358-369	12
α-helix	371-2144	9

Chain B: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1012-1019	8
β-strand	1029	1	10
β-strand	1030	1	11
α-helix	1035	1
β-strand	1036	1	10
α-helix	1037-1038	2
α-helix	1039-1047	9
β-strand	1053-1055	3	12
β-strand	1058-1060	3	12
β-strand	1061	1	11
α-helix	1064-1076	13
β-strand	1082-1083	2	13
α-helix	1085-1092	8
α-helix	1096-1098	3
β-strand	1102-1103	2	13
α-helix	1108	1
β-strand	1109	1	13
α-helix	1110-1111	2
α-helix	1112-1120	9
α-helix	1123-1124	2
β-strand	1125-1128	4	13
β-strand	1131-1134	4	13
α-helix	1138-1140	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3	A	protein	383	Escherichia coli (strain K12), Homo sapiens	P0AEX9 (AlphaFold model), Q14653 (AlphaFold model)
Protein E6	B	protein	153	Human papillomavirus type 16	P03126 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SIV_1 Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3 (chains A)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSA
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAAAEDILDELLGEER

Sequence of entity 2 (B), FASTA

>6SIV_2 Protein E6 (chains B)
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFARRDLCIVYRDGN
PYAVCDKCLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRH
LDKKQRFHNIRGRWTGRCMSCSRSSRTRRETQL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Deciphering the molecular and structural interaction between IRF3 and HPV16 E6. Poirson, J., Suarez, I.P., Cousido-Siah, A. et al. To be published.

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

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